macs for rip-seq

[Gao Fan]

Hi Tao,

I have some RIP-seq data generated by a modified immuno-precipitation protocol which used sonication step for fragmentation followed by IP just like ChIP-Seq. I wonder if MACS can be applied here for peak calling?

Thanks,

Fan

[sinobio]

try this one: RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.

2013/8/13 Gao Fan <gaof...@hotmail.com>

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[Tao Liu]

Hi Fan,

Answer is NO:

The "background" of RIP-seq is not the genome sequence, instead it's the RNA sequences. If you consider alternative splicing, things will become more complicated. Although you can still use MACS if you construct a 'genome' of RNA sequences (mRNA?), map reads to these sequences then call peaks. You should try something specifically designed for RIP-seq analysis if possible.

Best,

Tao Liu

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Assistant Professor
Department of Biochemistry
University at Buffalo
NY State Center of Excellence in Bioinformatics & Life Sciences

B2-163 COEBLS
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tl...@buffalo.edu

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[Ian Donaldson]

ASPeak was published the other day - could be useful...
http://view.ncbi.nlm.nih.gov/pubmed/23929032

Ian

[Gao Fan]

Thanks a lot.

Fan

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Date: Fri, 16 Aug 2013 10:12:33 +0100
Subject: Re: [macs-announscement] macs for rip-seq
From: donald...@gmail.com
To: macs-ann...@googlegroups.com